AssemblyManager
Note: this document is automatically generated from mobx-state-tree objects in our source code. See Core concepts and intro to pluggable elements for more info
Also note: this document represents the state model API for the current released version of jbrowse. If you are not using the current version, please cross reference the markdown files in our repo of the checked out git tag
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AssemblyManager - Properties
property: assemblies
this is automatically managed by an autorun which looks in the parent session.assemblies, session.sessionAssemblies, and session.temporaryAssemblies
// type signature
IArrayType<IModelType<{ configuration: IMaybe<IReferenceType<IAnyType>>; }, { error: unknown; loadingP: Promise<void> | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 5 m...
// code
assemblies: types.array(assemblyFactory(conf, pm))
AssemblyManager - Getters
getter: assemblyNameMap
// type
Record<string, { configuration: any; } & NonEmptyObject & { error: unknown; loadingP: Promise<void> | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 6 more ... & IStateTr...
getter: assemblyNamesList
// type
any
getter: assemblyList
combined jbrowse.assemblies, session.sessionAssemblies, and session.temporaryAssemblies
// type
({ [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({ [x: string]: any; } & NonEmptyObject & ... & IStateTreeNode<...>); } & IStateTreeNode<...>)[]
AssemblyManager - Methods
method: get
// type signature
get: (asmName: string) => { configuration: any; } & NonEmptyObject & { error: unknown; loadingP: Promise<void> | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 6 more ... & IS...
method: waitForAssembly
use this method instead of assemblyManager.get(assemblyName) to get an assembly with regions loaded
// type signature
waitForAssembly: (assemblyName: string) => Promise<{ configuration: any; } & NonEmptyObject & { error: unknown; loadingP: Promise<void> | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 6 ...
method: getRefNameMapForAdapter
// type signature
getRefNameMapForAdapter: (adapterConf: AdapterConf, assemblyName: string, opts: { stopToken?: string; sessionId: string; }) => Promise<any>
method: getReverseRefNameMapForAdapter
// type signature
getReverseRefNameMapForAdapter: (adapterConf: AdapterConf, assemblyName: string, opts: { stopToken?: string; sessionId: string; }) => Promise<any>
method: isValidRefName
// type signature
isValidRefName: (refName: string, assemblyName: string) => boolean
AssemblyManager - Actions
action: removeAssembly
private: you would generally want to add to manipulate jbrowse.assemblies, session.sessionAssemblies, or session.temporaryAssemblies instead of using this directly
// type signature
removeAssembly: (asm: { configuration: any; } & NonEmptyObject & { error: unknown; loadingP: Promise<void> | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 6 more ... & IStateTreeNode<.....
action: addAssembly
private: you would generally want to add to manipulate jbrowse.assemblies, session.sessionAssemblies, or session.temporaryAssemblies instead of using this directly
this can take an active instance of an assembly, in which case it is referred to, or it can take an identifier e.g. assembly name, which is used as a reference. snapshots cannot be used
// type signature
addAssembly: (configuration: any) => void